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      LIGGGHTS tips
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        <p>本篇介绍几个 LIGGGHTS 技巧，read_data，freeze，move，modify_timing，neigh_modify。</p>
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<p>LIGGGHTS 中可以用 STL 格式的几何面来模拟复杂边界的问题。如果想用冻结粒子当作壁面，可以采用如下方法。<br><figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br></pre></td><td class="code"><pre><span class="line"><span class="built_in">read</span>_data test.dat</span><br><span class="line"></span><br><span class="line">group    Par_wall id &lt;&gt; <span class="number">1</span> <span class="number">1000</span>  </span><br><span class="line">fix       fr Par_wall freeze</span><br></pre></td></tr></table></figure></p>
<p>上述代码中，第一行是从外部文件中读取颗粒的信息；第二行是将ID在 1 到 1000 的粒子放到一个 group 里；第三行是将 Par_wall 这个 group 里的粒子冻结起来，具体的操作其实是将这些粒子的力归零，这样粒子将保持最初始的速度。如果将壁面粒子预先生成好，并将其初始速度设置为 0，便可以实现冻结粒子壁面了。</p>
<p>test.data 文件的数据格式如下，每一列数据的含义见注释：<br><figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br></pre></td><td class="code"><pre><span class="line">LAMMPS data file via write_data, version Version LIGGGHTS-PUBLIC <span class="number">3.2</span>.<span class="number">0</span>, git commit <span class="number">6</span>de550fbf3b8451f51246aa3c76374012e935340 based on LAMMPS <span class="number">23</span> Nov <span class="number">2013</span>, timestep = <span class="number">0</span>  <span class="comment">## 第一行随便是什么</span></span><br><span class="line"></span><br><span class="line"><span class="number">5</span> atoms  <span class="comment">## 颗粒数</span></span><br><span class="line"><span class="number">1</span> atom types <span class="comment">## 颗粒的 type 数</span></span><br><span class="line"></span><br><span class="line"><span class="comment">## 模拟区域的大小</span></span><br><span class="line">-<span class="number">5.0009999999999999</span>e-<span class="number">01</span> <span class="number">5.0009999999999999</span>e-<span class="number">01</span> xlo xhi</span><br><span class="line">-<span class="number">2.0004000000000002</span>e-<span class="number">01</span> <span class="number">2.0004000000000002</span>e-<span class="number">01</span> ylo yhi</span><br><span class="line">-<span class="number">2.0005500000000001</span>e-<span class="number">01</span> <span class="number">3.4999999999999998</span>e-<span class="number">01</span> zlo zhi</span><br><span class="line"></span><br><span class="line">Atoms</span><br><span class="line"><span class="comment">#id type diameter density x y z i j k</span></span><br><span class="line"><span class="number">1</span> <span class="number">1</span> <span class="number">2.9999999999999999</span>e-<span class="number">02</span> <span class="number">2.5000000000000005</span>e+<span class="number">03</span> -<span class="number">2.9626205235821884</span>e-<span class="number">01</span> -<span class="number">1.7191257603378007</span>e-<span class="number">01</span> -<span class="number">5.2585560979625336</span>e-<span class="number">02</span> <span class="number">0</span> <span class="number">0</span> <span class="number">0</span></span><br><span class="line"><span class="number">2</span> <span class="number">1</span> <span class="number">2.9999999999999999</span>e-<span class="number">02</span> <span class="number">2.5000000000000005</span>e+<span class="number">03</span> -<span class="number">3.1357080694177836</span>e-<span class="number">01</span> -<span class="number">8.1292507237863978</span>e-<span class="number">02</span> -<span class="number">3.0941241635135643</span>e-<span class="number">02</span> <span class="number">0</span> <span class="number">0</span> <span class="number">0</span></span><br><span class="line"><span class="number">3</span> <span class="number">1</span> <span class="number">2.9999999999999999</span>e-<span class="number">02</span> <span class="number">2.5000000000000005</span>e+<span class="number">03</span> -<span class="number">3.4986005571676082</span>e-<span class="number">01</span> -<span class="number">4.6564797686740017</span>e-<span class="number">02</span> -<span class="number">5.0161637377833301</span>e-<span class="number">02</span> <span class="number">0</span> <span class="number">0</span> <span class="number">0</span></span><br><span class="line"><span class="number">4</span> <span class="number">1</span> <span class="number">2.9999999999999999</span>e-<span class="number">02</span> <span class="number">2.5000000000000005</span>e+<span class="number">03</span> -<span class="number">3.2901105748658366</span>e-<span class="number">01</span> <span class="number">1.1629149478965480</span>e-<span class="number">01</span> -<span class="number">2.8537062345934828</span>e-<span class="number">02</span> <span class="number">0</span> <span class="number">0</span> <span class="number">0</span></span><br><span class="line"><span class="number">5</span> <span class="number">1</span> <span class="number">5.0000000000000003</span>e-<span class="number">02</span> <span class="number">2.5000000000000000</span>e+<span class="number">03</span> -<span class="number">3.9692279707164302</span>e-<span class="number">01</span> <span class="number">1.5000972515153915</span>e-<span class="number">01</span> -<span class="number">3.5647118241865984</span>e-<span class="number">02</span> <span class="number">0</span> <span class="number">0</span> <span class="number">0</span></span><br><span class="line"></span><br><span class="line"></span><br><span class="line">Velocities <span class="comment">## 如果粒子的初始速度为零，这一段可以删去。</span></span><br><span class="line"><span class="comment">#id vx vy vz omegax omegay omegaz</span></span><br><span class="line"><span class="number">1</span> -<span class="number">1.5290519507823870</span>e+<span class="number">00</span> <span class="number">1.0245516532619933</span>e-<span class="number">01</span> -<span class="number">1.1594445288149451</span>e+<span class="number">00</span> <span class="number">6.3791250045904881</span>e+<span class="number">00</span> <span class="number">2.0674456758001139</span>e+<span class="number">02</span> <span class="number">1.0276923966595568</span>e+<span class="number">02</span></span><br><span class="line"><span class="number">2</span> -<span class="number">2.1385398568904033</span>e+<span class="number">00</span> -<span class="number">1.8858415304542153</span>e-<span class="number">01</span> -<span class="number">9.4897293591801291</span>e-<span class="number">01</span> <span class="number">1.2732686070189061</span>e+<span class="number">01</span> <span class="number">1.9114652955524940</span>e+<span class="number">02</span> -<span class="number">4.8862922016708987</span>e+<span class="number">00</span></span><br><span class="line"><span class="number">3</span> -<span class="number">2.1931823490540205</span>e+<span class="number">00</span> <span class="number">1.2314081721772643</span>e-<span class="number">01</span> -<span class="number">1.1305039942880526</span>e+<span class="number">00</span> -<span class="number">7.7211996358126047</span>e+<span class="number">00</span> <span class="number">1.8655504536271400</span>e+<span class="number">02</span> -<span class="number">3.5674698533544941</span>e+<span class="number">01</span></span><br><span class="line"><span class="number">4</span> -<span class="number">2.3661710510727509</span>e+<span class="number">00</span> <span class="number">6.5301832663338024</span>e-<span class="number">03</span> -<span class="number">9.2367025774174294</span>e-<span class="number">01</span> -<span class="number">5.7926985652143115</span>e-<span class="number">01</span> <span class="number">1.7594397127744105</span>e+<span class="number">02</span> <span class="number">6.1151183183219171</span>e+<span class="number">00</span></span><br><span class="line"><span class="number">5</span> -<span class="number">2.6032940321288258</span>e+<span class="number">00</span> <span class="number">1.7791968545582579</span>e-<span class="number">01</span> -<span class="number">1.0893683893889663</span>e+<span class="number">00</span> -<span class="number">1.6450273309025711</span>e+<span class="number">01</span> <span class="number">6.8599979334439681</span>e+<span class="number">01</span> <span class="number">3.4617478295022179</span>e+<span class="number">00</span></span><br></pre></td></tr></table></figure></p>
<p>上述能实现静止的壁面，如果希望用粒子来实现运动壁面（比如旋转），则可以用 move 命令：<br><figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br></pre></td><td class="code"><pre><span class="line">group rotateWall id &lt;&gt; <span class="number">1001</span> <span class="number">2000</span> <span class="comment"># 将 1001 &lt;= id &lt;= 2000 的粒子放到 group rotateWall 里</span></span><br><span class="line">fix mov rotateWall move rotate -<span class="number">19.8</span> <span class="number">0</span> <span class="number">0</span> <span class="number">1</span> <span class="number">0</span> <span class="number">0</span> <span class="number">8</span></span><br></pre></td></tr></table></figure></p>
<p>move 命令有不同的模式，这里用的是 rotate，用这个命令以后，rotateWall 这个 group 里的粒子，将按照指定的参数来进行旋转运动，而不再是根据其受力来更新速度和位置。参数的含义分别为：起始点坐标(x,y,z)；旋转轴的指向(x,y,z)；周期(转一圈的时间)。</p>
<p>最后再介绍几个小 tips：</p>
<ol>
<li>有时候想知道程序中哪一部分耗时最多，并据此来优化程序，这时可以在输入脚本的最开头，添加一句 modify_timing on ，之后在程序运行结束后会统计出每一条 fix 命令的耗时信息。</li>
<li>上述提到的冻结粒子壁面，在使用中会有一个问题：壁面粒子之间的距离通常是很小的，在建立粒子碰撞对的时候，壁面粒子之间通常会形成碰撞对，但壁面粒子之间没必要建立碰撞对，如果壁面粒子很多，这个建立过程是很耗时的。这种情况下，可以通过修改 neigh_modify 命令的参数来防止壁面粒子之间建立碰撞对：<figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br></pre></td><td class="code"><pre><span class="line">neigh_modify delay <span class="number">0</span> exclude group  Par_wall Par_wall</span><br></pre></td></tr></table></figure>
</li>
</ol>
<p>这条命令将防止在 Par_wall 这个 group 里的粒子彼此之间建立碰撞对。</p>

      
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